Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012498.1 Corchorus capsularis cultivar CVL-1 contig12519, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 16958
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:1053 original size:41 final size:41
Alignment explanation
Indices: 999--1081 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
989 TAGAGCTGTC
999 AAAAGCTGACCCGAGCCCGAGAATCCGCCCAACCCGTCCAA
1 AAAAGCTGACCCGAGCCCGAGAATCCGCCCAACCCGTCCAA
1040 AAAAGCTGACCCGAGCCCGAGAATCCGCCCAACCCGTCCAA
1 AAAAGCTGACCCGAGCCCGAGAATCCGCCCAACCCGTCCAA
1081 A
1 A
1082 TTCGAATCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.33, C:0.41, G:0.19, T:0.07
Consensus pattern (41 bp):
AAAAGCTGACCCGAGCCCGAGAATCCGCCCAACCCGTCCAA
Found at i:1177 original size:32 final size:32
Alignment explanation
Indices: 1141--1252 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 32
1131 CCGCCCGACT
* *
1141 CGAGACCCGAGTGACCCGCAACCCAGATGATC
1 CGAGACCCGAATGACCCGCAACCCAGATGACC
*
1173 CGAGACCCGAATGACCCGTAACCCAGATGACC
1 CGAGACCCGAATGACCCGCAACCCAGATGACC
* * * *
1205 CGAAACCCGAATGACCTGTAACTC-GAGTGACC
1 CGAGACCCGAATGACCCGCAACCCAGA-TGACC
*
1237 CGAGACCCGTATGACC
1 CGAGACCCGAATGACC
1253 GAAACCCGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 2 0.03
32 69 0.97
ACGTcount: A:0.29, C:0.36, G:0.23, T:0.12
Consensus pattern (32 bp):
CGAGACCCGAATGACCCGCAACCCAGATGACC
Found at i:1251 original size:16 final size:15
Alignment explanation
Indices: 1141--1272 Score: 83
Period size: 16 Copynumber: 8.3 Consensus size: 15
1131 CCGCCCGACT
1141 CGAGACCCGAGTGACC
1 CGAGACCCGA-TGACC
*
1157 CGCA-ACCCAGATGATC
1 CG-AGACCC-GATGACC
1173 CGAGACCCGAATGACC
1 CGAGACCCG-ATGACC
1189 CGTA-ACCCAGATGACC
1 CG-AGACCC-GATGACC
*
1205 CGAAACCCGAATGACC
1 CGAGACCCG-ATGACC
* *
1221 TGTA-ACTCGAGTGACC
1 CG-AGACCCGA-TGACC
1237 CGAGACCCGTATGA-C
1 CGAGACCCG-ATGACC
* *
1252 CGAAACCCGAATAACC
1 CGAGACCCG-ATGACC
1268 CGAGA
1 CGAGA
1273 AGTTAACCCG
Statistics
Matches: 93, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
15 18 0.19
16 68 0.73
17 7 0.08
ACGTcount: A:0.32, C:0.35, G:0.23, T:0.11
Consensus pattern (15 bp):
CGAGACCCGATGACC
Found at i:2131 original size:16 final size:16
Alignment explanation
Indices: 2112--2211 Score: 82
Period size: 16 Copynumber: 6.4 Consensus size: 16
2102 AGACCGGGTA
*
2112 GACCTGAGACCCGAAT
1 GACCCGAGACCCGAAT
* * *
2128 GACCCAAGATCCAAAT
1 GACCCGAGACCCGAAT
* *
2144 GACCCGAAACCCGTAT
1 GACCCGAGACCCGAAT
*
2160 GACCTGAGACCCGAA-
1 GACCCGAGACCCGAAT
*
2175 -ACCC-AAACCC-AGAT
1 GACCCGAGACCCGA-AT
*
2189 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
2205 GACCCGA
1 GACCCGA
2212 CAAAACTACC
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
12 1 0.02
13 6 0.09
14 3 0.05
15 4 0.06
16 50 0.77
17 1 0.02
ACGTcount: A:0.36, C:0.36, G:0.19, T:0.09
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:2190 original size:29 final size:30
Alignment explanation
Indices: 2145--2203 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2135 GATCCAAATG
* *
2145 ACCCGAAACCCGTATGACCTGAGACCCGAA
1 ACCCGAAACCCGTATGACCCGAAACCCGAA
2175 ACCC-AAACCCAG-ATGACCCGAAACCCGAA
1 ACCCGAAACCC-GTATGACCCGAAACCCGAA
2204 TGACCCGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.37, C:0.39, G:0.17, T:0.07
Consensus pattern (30 bp):
ACCCGAAACCCGTATGACCCGAAACCCGAA
Found at i:2201 original size:45 final size:47
Alignment explanation
Indices: 2112--2208 Score: 144
Period size: 45 Copynumber: 2.1 Consensus size: 47
2102 AGACCGGGTA
* *
2112 GACCTGAGACCCGAATGACCCAAGATCCAAATGACCCGAAACCCGTAT
1 GACCTGAGACCCGAA-GACCCAAGACCCAAATGACCCGAAACCCGAAT
*
2160 GACCTGAGACCCGAA-ACCCAA-ACCCAGATGACCCGAAACCCGAAT
1 GACCTGAGACCCGAAGACCCAAGACCCAAATGACCCGAAACCCGAAT
2205 GACC
1 GACC
2209 CGACAAAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 25 0.54
46 6 0.13
48 15 0.33
ACGTcount: A:0.36, C:0.36, G:0.19, T:0.09
Consensus pattern (47 bp):
GACCTGAGACCCGAAGACCCAAGACCCAAATGACCCGAAACCCGAAT
Found at i:6657 original size:3 final size:3
Alignment explanation
Indices: 6651--6684 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6641 TTCCTTGTTT
6651 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6685 CTACTCGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:9332 original size:41 final size:41
Alignment explanation
Indices: 9259--9336 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
9249 GAACAACTTT
**
9259 AGGCACAAACATTCTTTGTGCCCATATGTCAGGAACGACAC
1 AGGCACAAACATTCTTCCTGCCCATATGTCAGGAACGACAC
* * *
9300 AGGCACATACATTCTTCCTGCCTATATTTCAGGAACG
1 AGGCACAAACATTCTTCCTGCCCATATGTCAGGAACG
9337 GCACTACCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (41 bp):
AGGCACAAACATTCTTCCTGCCCATATGTCAGGAACGACAC
Found at i:11220 original size:17 final size:17
Alignment explanation
Indices: 11198--11233 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
11188 GAGCAAAAAT
11198 GCTAAAGCAG-AATCAGA
1 GCTAAAG-AGAAATCAGA
11215 GCTAAAGAGAAATCAGA
1 GCTAAAGAGAAATCAGA
11232 GC
1 GC
11234 ATTAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.47, C:0.17, G:0.25, T:0.11
Consensus pattern (17 bp):
GCTAAAGAGAAATCAGA
Found at i:12411 original size:18 final size:18
Alignment explanation
Indices: 12388--12428 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12378 TTCATCAACC
* *
12388 TCTTCATTAGATCTTTCT
1 TCTTCAGTAGATCCTTCT
*
12406 TCTTCAGTAGGTCCTTCT
1 TCTTCAGTAGATCCTTCT
12424 TCTTC
1 TCTTC
12429 CCCTTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.51
Consensus pattern (18 bp):
TCTTCAGTAGATCCTTCT
Done.